1. Redefining scrheadings
The redefinition of scrheading is described in chapter 5 in the KOMAscript-manual.
Add the following three lines to your MWE:
\clearscrheadfoot
\ohead{\rightmark}
\cfoot[\pagemark]{\pagemark}
You manipulate chapteror sectionin the header by changing between \leftmark and \rightmark in the second line, i.e.
\ohead{\rightmark} % section-names in the header
\ohead{\leftmark} % chapter-names in the header
If you use the option twoside to the class, you can use the command
\ohead{\headmark}
and have chapter names in the left-side heading and section names in the right-side headings, automagically.
Page number x of y
To have page number as ‘6 of 10’, add the package lastpage and redefine the cfoot to:
\cfoot[\pagemark]{\pagemark{} of \pageref{LastPage}}
NB! If you want the same page numbering in the part- and chapter-sides, add the same commands to the optional argument of \cfoot, i.e.
\cfoot[\pagemark{} of \pageref{LastPage}]% for pagestyle `scrplain`
{\pagemark{} of \pageref{LastPage}}% for pagestyle `scrheading`
3. Section number in heading
To remove the section (or chapter-) number from the heading, in KOMAscript you use the commands:
\renewcommand*{\sectionmarkformat}{}
and
\renewcommand*{\chaptermarkformat}{}
Unfortunately, this does not work in classicthesis (the spaced smallcaps disappear). Instead, you have to use
\renewcommand{\sectionmark[1]{\markright{\spacedlowsmallcaps{#1}}}
4. Complete MWE
Your MWE with all your requirements implemented:
\documentclass[dottedtoc, headinclude, footinclude=true]{scrreprt}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage[pdfspacing]{classicthesis}
\usepackage{lastpage,lipsum,kantlipsum} % Generates dummy text.
\pagestyle{scrheadings} % <--- Affects the page header
% and page number in the footer.
\clearscrheadfoot
\ohead{\rightmark} % comment this line and uncomment the next
% to switch to `chapter name` in the heading
%\ohead{\leftmark} % comment out to
\cfoot[\pagemark]{\pagemark}
\cfoot[\pagemark{} of \pageref{LastPage}]% for pagestyle `scrplain`
{\pagemark{} of \pageref{LastPage}}% for pagestyle `scrheading`
\renewcommand{\sectionmark}[1]{\markright{\spacedlowsmallcaps{#1}}}
% Remove section number from heading
\begin{document}
\tableofcontents
\part{Liechtenstein}
\chapter{Liechtenstein}\kant[1-6]\clearpage
\part{Germany}
\chapter{Germany}\kant[1-3]\clearpage
\section{Bavaria}\kant[1-6]\clearpage
\section{Hesse}\kant[1-6]
\end{document}
I do not see a problem with your MWE. The first chapter is on page 5, the same page number as the entry in the table of contents.
You mentioned \addcontentsline. If the command gets on the previous page, then also
the page number is taken from the previous page. Make sure that \addcontentsline is on the right page, e.g.:
\cleardoublepage
\addcontentsline{toc}{chapter}{Acknowledgments}
\chapter*{Acknowledgments}
or
\chapter*{Acknowledgments}
\addcontentsline{toc}{chapter}{Acknowledgments}
Best Answer
Add
dottedtocto the options when callingclassicthesis:where
...stands for the present options you're using.